LOCUS       NZ_CP103538             6062 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4238 plasmid pMB9108_5, complete sequence.
ACCESSION   NZ_CP103538
VERSION     NZ_CP103538.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174054
            Assembly: GCF_024917735.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6062)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 6062)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 186x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:16:44
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,040
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,655
            CDSs (with protein)               :: 4,655
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 86 of 267
            Pseudo Genes (incomplete)         :: 179 of 267
            Pseudo Genes (internal stop)      :: 42 of 267
            Pseudo Genes (multiple problems)  :: 39 of 267
            Pseudo Genes (short protein)      :: 4 of 267
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103538.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..6062
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4238"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9108_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-09-28"
                     /collected_by="MDACC"
                     /genotype="ST410"
     gene            join(5259..6062,1..495)
                     /locus_tag="M5T38_RS25010"
                     /old_locus_tag="M5T38_25010"
     CDS             join(5259..6062,1..495)
                     /locus_tag="M5T38_RS25010"
                     /old_locus_tag="M5T38_25010"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_052918197.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESSITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFLSGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            500..937
                     /locus_tag="M5T38_RS25015"
                     /old_locus_tag="M5T38_25015"
     CDS             500..937
                     /locus_tag="M5T38_RS25015"
                     /old_locus_tag="M5T38_25015"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052918195.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(1172..1285)
                     /locus_tag="M5T38_RS25020"
                     /old_locus_tag="M5T38_25020"
     CDS             complement(1172..1285)
                     /locus_tag="M5T38_RS25020"
                     /old_locus_tag="M5T38_25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072101919.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(1937..2128)
                     /locus_tag="M5T38_RS25025"
                     /old_locus_tag="M5T38_25025"
     CDS             complement(1937..2128)
                     /locus_tag="M5T38_RS25025"
                     /old_locus_tag="M5T38_25025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2193..2516
                     /locus_tag="M5T38_RS25030"
                     /old_locus_tag="M5T38_25030"
     CDS             2193..2516
                     /locus_tag="M5T38_RS25030"
                     /old_locus_tag="M5T38_25030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956001.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2725..>3156
                     /locus_tag="M5T38_RS25035"
                     /old_locus_tag="M5T38_25035"
                     /pseudo=""
     CDS             2725..>3156
                     /locus_tag="M5T38_RS25035"
                     /old_locus_tag="M5T38_25035"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3194..3712
                     /locus_tag="M5T38_RS25040"
                     /old_locus_tag="M5T38_25040"
     CDS             3194..3712
                     /locus_tag="M5T38_RS25040"
                     /old_locus_tag="M5T38_25040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_052918199.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPCGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            3719..3952
                     /locus_tag="M5T38_RS25045"
                     /old_locus_tag="M5T38_25045"
     CDS             3719..3952
                     /locus_tag="M5T38_RS25045"
                     /old_locus_tag="M5T38_25045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1765..1852
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          complement(1214..1751)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.814"
                     /coverage="99.0"
                     /evalue="3.760000000000001e-179"
     Typing          2507..4056
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagaattttg caaaaaatca aaaagtattt tctcttagag tcgtgaaaaa aactgctaat
       61 ggggagattt cggttcccat tgattttgaa tcagagggga ccaaaaagat agtctatctc
      121 cttgggccta tttataacgc catgattaac aataacttat tattggttga tgagttcgat
      181 tcaaagttcc ataccctttt atctaagttt ttatttagga tatttcatgc gcaaagtgaa
      241 gggtttagcc aagtaatcgc tgcagttcag gatgttaatt taatgaatac tgattgcttt
      301 agacgagacc aaatttggtt tgttgacaag gatgtaaagt cagggagtag ccatctttat
      361 tctttggttg agtacaaaga gaaacaaaga tcattgaagc catcatatgg gaatgattat
      421 ttatcaggtg cttttgatgc aatcccgtta tttgataatc ttaatgaatt tgaaaagcta
      481 atgcctgagg gatgattata tgccaaagag aggcaaaagc attcgaagct cttcgaggaa
      541 tgaggaaaca aaaccttcaa agagcacagc gaaaacgact gatagattta tatctattag
      601 ttttaagcat tttcataacg tcgatgatgt tgggcagtcc ataaatacat ggaaagatga
      661 tggtagccta cctgatctca ttgaaaaatt ggtttatcta acggcgaatg gaatcactaa
      721 agtgatttct gacggtgtgt ttactaacta cactcgattt cctgagtcag ctgtaaacga
      781 ttttagatgc ccagatgaga tatcctctga tgaggattgg ggggttataa aaaacattgg
      841 cgggcagaaa agaagagtcg ccggatttct gagagataat gtgttctata tcgtgttttt
      901 tgatagagat catcgcttct ggaagagtca aaaatagatg agatacagtt gtattgtatg
      961 ttaagaaaag atcttcttga gattgtgatg ctctcgtcgt aatctcttgc tctgtaaacg
     1021 aaaaaaccgc cttggcgggc ggtttttcga cggttctaag agttggcgct ctgtgaacca
     1081 aggtaactgg cttatgagga gcgcagtaac caaatctgtt ctttcagttt agccttaaca
     1141 ggcgcataac ttcaagacta actcctctaa atcagttacc agtggctgct gccattggcg
     1201 ttttgtcgtg tctttccggg ttggactcaa gttgatagtt accggaaaag gcgcagcggt
     1261 cggactgaac ggggggttcg tgcatacagt ccagcttgga gcgaactgcc tacccggaac
     1321 tgagtgtcag gcgtggaatg agacaaacgc ggccataaca gcggagtgac accggtaaac
     1381 cgaatggcag gaacaggaga gcgcacgagg gagtcaccag ggggaaacgc ctggtatctt
     1441 taagtcctgt cgggtttcgc cacctctgac ttgagcgtcg gtttttgtga tgctcgtcag
     1501 gggggcggag cctatggaaa aacgccagcg gcgcggcctt cctcctgttc ctggtctttt
     1561 gctcacatgt tctttccggc cttatcccct gattctgtgg ataactgtgt taccgttttt
     1621 gtgtgagtca gtaccgctcg ccgcagtcga acgaccgagc gtagcgagtc agtgagcgag
     1681 gaagcggaaa agcgccggga catgcatttt ctccttacgc atctgtgcgg catttcacac
     1741 ccggcatggc gtacttttca tacaatccgc actgatgccg catggttaag ccagtataca
     1801 ctccgctatc gctacgtgac tgggtcagag ctgcgccccg acacccgcta aaacctgctg
     1861 acgcgccctg acgggcttgt ctgctcccgg catccgctca cagacaagct gtgaccgtct
     1921 ccgggagctg catgtgtcag aggttttcac cgtcatcccc gaaacgtgcg aggcagctgc
     1981 ggtaaagctc atcggcgtgg tcgtgaagcg attcacagat atctgcctgt tcatctgcgt
     2041 ccagttcgtt gagcttctcc agcagcgtta atgtctggct tctgataaag cgggccatgt
     2101 taagggcggt tttttcctgt ttagtcactg atgcctccgt gtaaggggga tttctgttca
     2161 cgggagtaat gataccgatg aaacgcgaga ggatgctcac gatacgggtt actgatgatg
     2221 aacatgcccg gttactggaa cgctgtgagg gtaaacaact ggcggtatgg atgcggcggg
     2281 tctgcctggg tgagccggtt gcccgttccg ggaagctgcc gacactggca ccgccgttac
     2341 tgcgtcagct ggccgccatc ggaaataacc tgaatcagac agcccgtaag gtgaacagcg
     2401 ggcagtggtc ttccggtgac cgggttcagg tggtggccgc actgatggcc atcggggatg
     2461 agctgcgccg gctgcgtctg gccgtcaggg aacagggagt gcgggatgat agttaagttt
     2521 catgccaggg gaaaaggtgg tggcagtggt ccggttgatt acctgctggg aagggagcgt
     2581 aaccgggaag gggcaacggt gcttcagggt gatccggaag aagtccggga actcatcgat
     2641 gccacgccat ttgcgaagaa atacacgtca ggtgttctgt cgttcgcgga gaaggagctg
     2701 ccgccgggag ggcgtgaaaa agtgatggcg agttttgagc gtgtactgat gcccggtctc
     2761 gaaaagaatc agtacagcat cctgtgggtg gagcaccagg acaagggacg gcttgagctg
     2821 aattttgtca ttccgaacat ggagctacag accggaaaac gcctccagcc gtactacgac
     2881 cgtgcagaca ggccgagaat tgatgcctgg cagacgctgg tgaatcacca ttacgggctg
     2941 catgacccca acgccccgga gaaccgccgg acgctgactc tccctgataa cctgccggaa
     3001 aagaaacagg cgcttgctga gagcgttaca cgggggcttg atgtgcttta ccgtgccgga
     3061 gagataaaag gccgtcagga tgtgattcag gcgctcacag aggtgggact tgaagtggtc
     3121 agggtgacgc gaagcagtat cagcattgca gacccgaacg gcgggaggaa tatcagactg
     3181 aaaggagcgt tttatgagca atcttttacg gacgggcgcg gagttcgaga aaaagctgaa
     3241 agagagagcc gaatctacag agaaaatgct gaacaacgag ttcaggaggc tcggcgaatc
     3301 tgtaagcgag gctgtgacat caaacgagac gaaaatcaaa gacgctatag ccctgttcac
     3361 cgcctcgaca gaggagtcgc tgaaaaaaca ccgggaaggg gtgaaagagg cgatgatgca
     3421 gcacaggaag gacatgttaa agctggcagg gaatacgggc atgatgttac tggggatagt
     3481 ctttctcctg tttaccgcga gtggcgggac gctctggtat cttggcggga ggatacaggc
     3541 gaacctggaa gatatcagga agcaggaaga gacattgcag aaactgaacg cgaagacatg
     3601 gggcgtggag tttgtgcagg acgggaacag gaaattcctt gtccttccgt gcgggaaatc
     3661 agcggaggtg attccctttc aggggaaaga gtgggtacat ctgaaggagt gacacagagt
     3721 gacagagctg gaaatacatt tgctgaacgc cttagagcag ctgcaacagg actatatgca
     3781 gcggctgagc gaatgggaga gcgccttcgt ggaattgcag aagatgtttt cgcttacgca
     3841 acgggacaac gcgatgctga acgagcgggt catgcagttg agtcagcagg tgcagcactt
     3901 gagcgagcag acagaacgct tgagccagtt atacagcgag aactggagat aagagaggaa
     3961 cggttgatac aggagcgcga acatgtgtta tccctggaac gggagcgtca gccggaaata
     4021 caggaacgca cgctggatgg cccttcgctg ggatggtgaa accatgaaaa atggcagctt
     4081 cagtggatta agtgggggga atgtggcctg taccatctgg ttgcataggt attcatacgg
     4141 ttaaaattta tcaggcgcga tcgcggcatt ttttcgggtg gtttgttgcc atttttacct
     4201 gtctgctgcc gtgatcgcga tgaacgcgtt ttagcggtgc gtacaattcg gatgttatgg
     4261 taaatccagc tgattggcag gtataaaaaa gccgtccgta gacggcctag taagttactt
     4321 cgtctttgtc atcactacca attcccatcg gatgtcacct gggacattat gctgcctgtg
     4381 attttgcggt ggcaaaggat catctttatt gcacgtcact tcatcaccac agttcgtgca
     4441 gcggtaaatg ccggaagccg gacaagtatt tcccggctta tagtaatacc gccatacact
     4501 cccttcaggc tcggttgttt ttgttaaaaa tttcgctgtg ctatctacat aaaaggccat
     4561 gttgctttcc ttacataaac taagttaggg accgaagctt gcatgcttcg gtggttattg
     4621 ttttttcttt tcccgattaa ttgggatctt aaacattccc ccgttaggac gggttatccg
     4681 tttgcccttt accgttatgt aagggcgaaa aatgtatgcc tgaggctcgt ccgtctgcat
     4741 gttgcatttc ctattttcgc cacatgaatg ttgatttttg ctatcaaaat tgtactgtag
     4801 caaccaacag atcttgtggc tggctttatc aaagcacttg aggtggtact caagcgccgc
     4861 atttgcgtat ggtttgttac gggttagttc tggtggtaca ggctaaccca cttacttcaa
     4921 caatttttgc ttctcctcat tcatgtttca ctccctacgt atttttttac agtgtcagcg
     4981 ccactgagca taaacgcgac aaaaaggaac catccccacc cagataccga gtgaaaagcc
     5041 agcactgctg agctaatcac tgaggcaaat gggaccattt ggtatagaaa aaacttcata
     5101 tacacctctt tttaagctgg tcgttaactt atctactcat aatgtgctgt ctattggacc
     5161 cttttgttgt tttagtacgg ggttatgcta ttcttaatct agaattttgt caatattgtg
     5221 caatttttga gtttaagggt gttgttaggg gtgttcttat gatggttaac tttagtcttt
     5281 caaacgcatt ttccttcatg gaagctcaaa atatgagcat gttggcggtg tcgtcatcga
     5341 aagacgatat aaacttggct aatgtagtgt cagtaaggga tgagcggata ctgaagtctg
     5401 ctttgatttt cggagctaac gctagcggaa aatctaatct catgaagaca atatctttaa
     5461 tgaaagatat tgtcctgcat tctgtgcaag ctatcgaaag tagcattacg aagaatgtag
     5521 tccctttttt acttgatgag gcggggccta ctaaaccatc tgaaatggaa atgactttta
     5581 ttgcggatgg gattaaatac agatacggat tatctttatt tcaagggaag ataaaagaag
     5641 agtggttgta ctacacgcca aaaacaaggg agactattct ctttgagcga gatggtcaac
     5701 ttattgaaat aaataaagca gcatttagcg agtcaaatct ttttataaag gatggggtca
     5761 ttcagaagac aagagaagat gttccctttg tttctgttgt tgctggattt aatggggagc
     5821 actcaaagcg tgttgtgaat tggtttagta atgtggtatt tctttctggt tctaacgaag
     5881 gaatgtttac tggaattacc atgaagctta taaatgaatc tgaagatttt aaagcttggc
     5941 taaaaaaaat attaccagcc tttcagatta atgatattta tcttgatgaa gttgcgcctg
     6001 aatttccgtt tggcaacata aaaacagatg atgataattt aaaaaattta ttcagctcga
     6061 tt
//
